Supplementary Fig. S1 DAY 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 33 35 36 p2 p3 p4 p5 p6 p7 p8 p9 p10 p11 p12 p13a p14 p15 p16 p17 p18b p19 p20 p21b p22 p23 p24 p25 p26 p27 p28b p29 p30 p31 p32 p33 p34b p35 p36
SARS-CoV-2 positive SARS-CoV-2 positive Throat swabs Anal swabs Hospitalization SARS-CoV-2 negative SARS-CoV-2 negative Supplementary Fig. S2
p36 Indicator (Genus) p35 p34 Ⅰ
p33 Bacteroidetes|Alloprevotella p32 p31 Ⅱ p30 Bacteroidetes|Bacteroidales*
p29 Bacteroidetes|Porphyromonas p28 Fusobacteria|Fusobacterium p27 Proteobacteria|Neisseria p26 p25 Ⅲ p24 Proteobacteria|Pseudomonas p23 p22 Ⅳ p21
p20 Actinobacteria|Actinomycetales*
p19 Actinobacteria|Rothia p18 Candidatus Saccharibacteria|
COVID -19 P atients Saccharibacteria incertae sedis p17 * unclassified genera p16
p15
p14 p13
p12
p11
p10
p09
p08 p07 p06 p05 p04 p03
p02 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 Days after symptom onset Supplementary Fig. S3
p36
p35
p33 Indicator (Genus) p32 Ⅰ p29 Bacteroidetes|Bacteroides p27 Bacteroidetes|Parabacteroides p25 Firmicutes|Anaerostipes
p23 Firmicutes|Blautia Firmicutes|Coprococcus p20 Firmicutes|Dorea p17 Firmicutes|Faecalibacterium
COVID -19 P atients p15 Firmicutes|Finegoldia
p13 Firmicutes|Fusicatenibacter Firmicutes|Lachnospiraceae* p11 Firmicutes|Roseburia p08 p07 Ⅱ p06 Proteobacteria|Neisseria p05 Ⅲ
p04 Proteobacteria|Pseudomonas p03 * unclassified genera 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 Days after symptom onset Supplementary Fig. S4
a Female Male b 17−33 years old 39−59 years old >63 years old
1.00 0.8 4 PFDR = 2.65e-02 8 0.75 13 0.6 4 10 7 4 ercent ercent 27 23 0.50 0.4 2
17 2 2 actor P actor P 0.25 0.2 4 3 10 11 1 1 F F 2 3 2 0.00 0.0 A(N = 16) B(N = 44) C(N = 10) D(N = 4) NP(N = 6) A(N = 16) B(N = 44) C(N = 10) D(N = 4) NP(N = 6) c d Virus detection Negative Positive Antibiotic Uses No Yes
12 3 3 11 0.6 29 0.6 4 3 5 23 5 5 ercent ercent 0.4 4 0.4 21 15 2 5 2 0.2 4 1 0.2 1 actor P actor P F F
0.0 0.0 A(N = 16) B(N = 44) C(N = 10) D(N = 4) NP(N = 5) A(N = 16) B(N = 44) C(N = 10) D(N = 4) NP(N = 6) Supplementary Fig. S5 a b Female Male 17−33 years old 39−59 years old >63 years old
0.8 1.00 12 6 0.6 16 4 0.75
ercent 0.4 0.50 9 8 2 11 0.2 0.25 8 actor P 3 4 F Factor Percent 5 2 0.0 0.00 A(N = 15) B(N = 24) C(N = 6) A(N = 15) B(N = 24) C(N = 6) c d Virus detection Negative Positive Antibiotic Uses No Yes
0.8 12 13 22 19 0.75 5 0.6 4
ercent 0.50 0.4 2 0.25
actor P 0.2 F Factor Percent 3 5 2 1 0.00 2 0.0 A(N = 15) B(N = 24) C (N = 6) A(N = 15) B(N = 24) C(N = 6) Supplementary Fig. S6
Throat indicator Gut indicator Ⅰ Haemophilus Parasutterella Alloprevotella Ruminococcus Ruminococcaceae* Roseburia Peptoniphilus Lachnospiracea Lachnospiracea incertae sedis Fusicatenibacter Finegoldia Faecalibacterium Ⅰ Dorea Coprococcus Clostridium Blautia Anaerostipes Anaerococcus Parabacteroides Bacteroides Corynebacterium
Porphyromonas Pasteurellaceae* Peptostreptococcus Neisseria Ⅱ Neisseria Campylobacter Fusobacterium Leptotrichiaceae* Bacteroidales* Leptotrichia Fusobacterium Streptococcus Ⅱ Oribacterium Lactobacillales* Lachnoanaerobaculum Gemella Porphyromonas Capnocytophaga Actinomyces
Ⅲ Pseudomonas Pseudomonas Ⅲ
Saccharibacteria *Unclassfied genera Ⅳ incertae sedis Rothia Actinomycetales* Supplementary Fig. S7 SARS-CoV-2
Respiratory tract
Epithelial Cells Faecalibacterlum Bacteroidales Prevotella Saccharibacteria sedis Comamonadaceae Bifidobacterium Fusobacterium Neisseria Pseudomonas Bacteroides Alloprevotella Porphyromonas Rothia s Ax i
t High diversity u G -
y Ⅰ Ⅱ Ⅲ/Ⅳ a w
r Low diversity A i (Dysbiosis)
Normal gut dominant butyrate-producing bacteria Resident microbiome Roseburia Faecalibacterlum Blautia Neisseria Pseudomonas Lachnospiraceae Coprococcus Bifidobacterium Bacteroides ……
ACE2
Epithelial Cells Gut
Healthy COVID-19 Days a�er symptom onset